Chemical Components in the PDB

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AIR : Summary

Code

AIR

One-letter code

X

Molecule name

5-AMINOIMIDAZOLE RIBONUCLEOTIDE

Systematic names

ProgramVersionName
ACDLabs 10.04 1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazol-5-amine
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R)-5-(5-aminoimidazol-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C8 H14 N3 O7 P

Formal charge

0

Molecular weight

295.186 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OCC2OC(n1cncc1N)C(O)C2O
SMILES CACTVS 3.341 Nc1cncn1[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
SMILES OpenEye OEToolkits 1.5.0 c1c(n(cn1)C2C(C(C(O2)COP(=O)(O)O)O)O)N
Canonical SMILES CACTVS 3.341 Nc1cncn1[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1c(n(cn1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N

IUPAC InChI

InChI=1S/C8H14N3O7P/c9-5-1-10-3-11(5)8-7(13)6(12)4(18-8)2-17-19(14,15)16/h1,3-4,6-8,12-13H,2,9H2,(H2,14,15,16)/t4-,6-,7-,8-/m1/s1

IUPAC InChI key

PDACUKOKVHBVHJ-XVFCMESISA-N
AIR

wwPDB Information

Atom count

33 (19 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-10-21

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



AIR : Atoms of Molecule

Total Number of Atoms: 33
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N Y N 0 -0.783 0.044 2.707
2 C2 C C2 N Y N 0 -1.831 -0.778 2.425
3 N3 N N3 N Y N 0 -2.561 -0.906 3.498
4 C4 C C4 N Y N 0 -2.02 -0.188 4.494
5 C5 C C5 N Y N 0 -0.903 0.412 4.021
6 N6 N N6 N N N 0 -0.043 1.25 4.733
7 C1' C C1' R N N 0 0.276 0.452 1.782
8 C2' C C2' R N N 0 1.44 -0.563 1.816
9 C3' C C3' S N N 0 1.913 -0.639 0.345
10 C4' C C4' R N N 0 0.981 0.341 -0.4
11 O4' O O4' N N N 0 -0.204 0.42 0.42
12 O2' O O2' N N N 0 2.496 -0.096 2.658
13 O3' O O3' N N N 0 3.274 -0.219 0.234
14 C5' C C5' N N N 0 0.633 -0.201 -1.787
15 O5' O O5' N N N 0 -0.284 0.685 -2.429
16 P P P N N N 0 -0.605 0.056 -3.876
17 O6 O O6 N N N 0 -1.64 1.009 -4.659
18 O7 O O7 N N N 0 0.758 -0.064 -4.723
19 O8 O O8 N N N 0 -1.202 -1.287 -3.708
20 HC2 H HC2 N N N 0 -2.027 -1.244 1.471
21 HC4 H HC4 N N N 0 -2.408 -0.105 5.499
22 HN61 H 1HN6 N N N 0 -0.223 1.451 5.665
23 HN62 H 2HN6 N N N 0 0.736 1.629 4.297
24 HC1' H HC1' N N N 0 0.636 1.449 2.034
25 HC2' H HC2' N N N 0 1.085 -1.537 2.154
26 HC3' H HC3' N N N 0 1.793 -1.65 -0.043
27 HC4' H HC4' N N N 0 1.45 1.321 -0.483
28 HO'2 H 2HO' N N N 0 3.213 -0.74 2.59
29 HO'3 H 3HO' N N N 0 3.807 -0.866 0.716
30 HC51 H 1HC5 N N N 0 1.541 -0.279 -2.385
31 HC52 H 2HC5 N N N 0 0.178 -1.186 -1.688
32 HO6 H HO6 N N N 0 -1.804 0.597 -5.518
33 HO7 H HO7 N N N 0 1.114 0.83 -4.809



AIR : Chemical Bonds

Total Number of Bonds: 34
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C2 N C sing 1.36 N Y
2 N1 C5 N C sing 1.37 N Y
3 N1 C1' N C sing 1.46 N N
4 C2 N3 C N doub 1.3 N Y
5 C2 HC2 C H sing 1.08 N N
6 N3 C4 N C sing 1.34 N Y
7 C4 C5 C C doub 1.35 N Y
8 C4 HC4 C H sing 1.08 N N
9 C5 N6 C N sing 1.4 N N
10 N6 HN61 N H sing 0.97 N N
11 N6 HN62 N H sing 0.97 N N
12 C1' C2' C C sing 1.54 N N
13 C1' O4' C O sing 1.44 N N
14 C1' HC1' C H sing 1.09 N N
15 C2' C3' C C sing 1.55 N N
16 C2' O2' C O sing 1.43 N N
17 C2' HC2' C H sing 1.09 N N
18 C3' C4' C C sing 1.54 N N
19 C3' O3' C O sing 1.43 N N
20 C3' HC3' C H sing 1.09 N N
21 C4' O4' C O sing 1.44 N N
22 C4' C5' C C sing 1.53 N N
23 C4' HC4' C H sing 1.09 N N
24 O2' HO'2 O H sing 0.97 N N
25 O3' HO'3 O H sing 0.97 N N
26 C5' O5' C O sing 1.43 N N
27 C5' HC51 C H sing 1.09 N N
28 C5' HC52 C H sing 1.09 N N
29 O5' P O P sing 1.61 N N
30 P O6 P O sing 1.61 N N
31 P O7 P O sing 1.61 N N
32 P O8 P O doub 1.48 N N
33 O6 HO6 O H sing 0.97 N N
34 O7 HO7 O H sing 0.97 N N



AIR : Used in PDB Entries

Total Number of PDB Entries: 11
Ligand Code PDB Entry ID Type Total Distinct
AIR 1d7a Open in New Window Bound ligand 4 1
AIR 2fwi Open in New Window Bound ligand 1 1
AIR 2fwj Open in New Window Bound ligand 1 1
AIR 3k5i Open in New Window Bound ligand 4 1
AIR 3r5h Open in New Window Bound ligand 2 1
AIR 3rgg Open in New Window Bound ligand 4 1
AIR 4fe2 Open in New Window Bound ligand 2 1
AIR 4s27 Open in New Window Bound ligand 1 1
AIR 4s28 Open in New Window Bound ligand 1 1
AIR 5cli Open in New Window Bound ligand 1 1
AIR 5clj Open in New Window Bound ligand 1 1